Whole-Genome Sequencing of Corallococcus sp. Strain EGB Reveals the Genetic Determinants Linking Taxonomy and Predatory Behavior

Abstract

Corallococcus sp. strain EGB is a Gram-negative myxobacteria isolated from saline soil, and has considerable potential for the biocontrol of phytopathogenic fungi. However, the detailed mechanisms related to development and predatory behavior are unclear. To obtain a comprehensive overview of genetic features, the genome of strain EGB was sequenced, annotated, and compared with 10 other Corallococcus species. The strain EGB genome was assembled as a single circular chromosome of 9.4 Mb with 7916 coding genes. Phylogenomics analysis showed that strain EGB was most closely related to Corallococcus interemptor AB047A, and it was inferred to be a novel species within the Corallococcus genus. Comparative genomic analysis revealed that the pan-genome of Corallococcus genus was large and open. Only a small proportion of genes were specific to strain EGB, and most of them were annotated as hypothetical proteins. Subsequent analyses showed that strain EGB produced abundant extracellular enzymes such as chitinases and β-(1,3)-glucanases, and proteases to degrade the cell-wall components of phytopathogenic fungi. In addition, 35 biosynthetic gene clusters potentially coding for antimicrobial compounds were identified in the strain EGB, and the majority of them were present in the dispensable pan-genome with unexplored metabolites. Other genes related to secretion and regulation were also explored for strain EGB. This study opens new perspectives in the greater understanding of the predatory behavior of strain EGB, and facilitates a potential application in the biocontrol of fungal plant diseases in the future.

Genome analysis of a plasmid-bearing myxobacterim Myxococcus sp. strain MxC21 with salt-tolerant property

“…Whole-genome phylogeny was performed to confirm the taxonomic classification. Based on the clustering results of orthologous proteins, we randomly selected 135 single-copy genes that conserved in all nine species (Edgar, 2004 ; Zhao et al, 2021 ). Alignments of the concatenated sequences of 135 single-copy genes were generated by the Muscle algorithm, and then, the phylogenetic tree was constructed by the neighbor joining algorithm with 1,000 bootstrap replicates in MEGA11 (Kumar et al, 2016 ).…”

Concepts and conjectures concerning predatory performance of myxobacteria

“…Comparative genome analysis of candidate biocontrol agent Corallococcus sp. strain EGB revealed that abundant extracellular chitinases, β-(1,3)-glucanases, and proteases are likely involved in the predation of phytopathogenic fungi ( Zhou et al, 2019 ; Zhao et al, 2021 ). Investigation of myxobacterial response to prey quorum signals revealed that oxidative degradation of toxic alkyl quinolones produced by P. aeruginosa benefits myxobacterium Cystobacter ferrugineus predation of the opportunistic pathogen ( Akbar et al, 2022 ; Figure 1A ).…”

Hayvancılık İşletmesi ve Termal Kaynak Kökenli Toprak ve Su Örneklerinden Miksobakteri İzolasyonu ve İzolatların Antibakteriyel Aktivitesi

“…Biyoteknolojik gelişmeler kültür olarak elde edilmesinin zor olduğu ya da hiç elde edilemeyeceği düşünülen mikroorganizmaların geleceğine umut olmuştur. Bunlardan biri de miksobakterilerdir [6] ve sahip oldukları genomik özelliklerinden dolayı ikincil metabolit üretimi açısından çok önemli bir grup olduğu görülmektedir [7][8][9].…”